[2024-01-24 13:01:11,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:11,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:11,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg2685a930-589f-4e72-a594-9c18101d4fd9/dqc_reference
[2024-01-24 13:01:12,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:12,724] [INFO] Task started: Prodigal
[2024-01-24 13:01:12,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e7c1cc5-1da4-47a5-8151-af8da16e667e/GCF_902459585.1_LMG_31109_genomic.fna.gz | prodigal -d GCF_902459585.1_LMG_31109_genomic.fna/cds.fna -a GCF_902459585.1_LMG_31109_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:28,433] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:28,433] [INFO] Task started: HMMsearch
[2024-01-24 13:01:28,433] [INFO] Running command: hmmsearch --tblout GCF_902459585.1_LMG_31109_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2685a930-589f-4e72-a594-9c18101d4fd9/dqc_reference/reference_markers.hmm GCF_902459585.1_LMG_31109_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:28,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:28,758] [INFO] Found 6/6 markers.
[2024-01-24 13:01:28,813] [INFO] Query marker FASTA was written to GCF_902459585.1_LMG_31109_genomic.fna/markers.fasta
[2024-01-24 13:01:28,814] [INFO] Task started: Blastn
[2024-01-24 13:01:28,814] [INFO] Running command: blastn -query GCF_902459585.1_LMG_31109_genomic.fna/markers.fasta -db /var/lib/cwl/stg2685a930-589f-4e72-a594-9c18101d4fd9/dqc_reference/reference_markers.fasta -out GCF_902459585.1_LMG_31109_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:29,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:29,839] [INFO] Selected 20 target genomes.
[2024-01-24 13:01:29,839] [INFO] Target genome list was writen to GCF_902459585.1_LMG_31109_genomic.fna/target_genomes.txt
[2024-01-24 13:01:29,846] [INFO] Task started: fastANI
[2024-01-24 13:01:29,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7c1cc5-1da4-47a5-8151-af8da16e667e/GCF_902459585.1_LMG_31109_genomic.fna.gz --refList GCF_902459585.1_LMG_31109_genomic.fna/target_genomes.txt --output GCF_902459585.1_LMG_31109_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:55,785] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:55,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2685a930-589f-4e72-a594-9c18101d4fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:55,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2685a930-589f-4e72-a594-9c18101d4fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:55,801] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:55,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:55,802] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	100.0	1602	1602	95	conclusive
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	89.1429	1363	1602	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	89.1205	1384	1602	95	below_threshold
Pandoraea pnomenusa	strain=DSM 16536	GCA_000767615.3	93220	93220	type	True	85.1985	1253	1602	95	below_threshold
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	85.1948	1251	1602	95	below_threshold
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	85.0319	1242	1602	95	below_threshold
Pandoraea terrigena	strain=LMG 31013	GCA_902459705.1	2508292	2508292	type	True	84.8567	1132	1602	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.8521	1249	1602	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	84.7615	1281	1602	95	below_threshold
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	84.7099	1144	1602	95	below_threshold
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	84.59	1259	1602	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	84.4901	1249	1602	95	below_threshold
Pandoraea vervacti	strain=NS15	GCA_000934605.2	656178	656178	type	True	84.3981	1261	1602	95	below_threshold
Pandoraea captiosa	strain=LMG 31118	GCA_902459775.1	2508302	2508302	type	True	84.3279	1297	1602	95	below_threshold
Pandoraea pneumonica	strain=LMG 31114	GCA_902459645.1	2508299	2508299	type	True	83.9859	1216	1602	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.8948	648	1602	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.6898	556	1602	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	78.5732	474	1602	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.4999	560	1602	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.4195	474	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:55,804] [INFO] DFAST Taxonomy check result was written to GCF_902459585.1_LMG_31109_genomic.fna/tc_result.tsv
[2024-01-24 13:01:55,805] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:55,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:55,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2685a930-589f-4e72-a594-9c18101d4fd9/dqc_reference/checkm_data
[2024-01-24 13:01:55,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:55,855] [INFO] Task started: CheckM
[2024-01-24 13:01:55,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459585.1_LMG_31109_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459585.1_LMG_31109_genomic.fna/checkm_input GCF_902459585.1_LMG_31109_genomic.fna/checkm_result
[2024-01-24 13:02:44,781] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:44,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:44,803] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:44,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:44,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459585.1_LMG_31109_genomic.fna/markers.fasta)
[2024-01-24 13:02:44,803] [INFO] Task started: Blastn
[2024-01-24 13:02:44,803] [INFO] Running command: blastn -query GCF_902459585.1_LMG_31109_genomic.fna/markers.fasta -db /var/lib/cwl/stg2685a930-589f-4e72-a594-9c18101d4fd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459585.1_LMG_31109_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:46,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:46,715] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:46,715] [INFO] Target genome list was writen to GCF_902459585.1_LMG_31109_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:46,739] [INFO] Task started: fastANI
[2024-01-24 13:02:46,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7c1cc5-1da4-47a5-8151-af8da16e667e/GCF_902459585.1_LMG_31109_genomic.fna.gz --refList GCF_902459585.1_LMG_31109_genomic.fna/target_genomes_gtdb.txt --output GCF_902459585.1_LMG_31109_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:06,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:06,395] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:06,395] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_902459585.1	s__Pandoraea nosoerga	100.0	1602	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.66	99.29	0.94	0.91	4	conclusive
GCF_000815105.2	s__Pandoraea pulmonicola	89.1263	1383	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000767615.3	s__Pandoraea pnomenusa	85.1833	1255	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	-
GCF_902459725.1	s__Pandoraea eparura	85.0684	1128	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459805.1	s__Pandoraea bronchicola	84.8898	1252	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459705.1	s__Pandoraea terrigena	84.8657	1131	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459735.1	s__Pandoraea capi	84.8521	1249	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_902459565.1	s__Pandoraea aquatica	84.7642	1280	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459745.1	s__Pandoraea communis	84.7168	1247	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_000807775.2	s__Pandoraea fibrosis	84.7085	1250	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	-
GCF_902459615.1	s__Pandoraea commovens	84.59	1259	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029105.3	s__Pandoraea faecigallinarum	84.5231	1273	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972785.3	s__Pandoraea oxalativorans	84.4874	1249	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934605.2	s__Pandoraea vervacti	84.3951	1261	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459775.1	s__Pandoraea captiosa	84.3307	1296	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459645.1	s__Pandoraea pneumonica	83.9802	1217	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:06,397] [INFO] GTDB search result was written to GCF_902459585.1_LMG_31109_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:06,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:06,401] [INFO] DFAST_QC result json was written to GCF_902459585.1_LMG_31109_genomic.fna/dqc_result.json
[2024-01-24 13:03:06,401] [INFO] DFAST_QC completed!
[2024-01-24 13:03:06,401] [INFO] Total running time: 0h1m55s